Add chrM example

Author: jeromekelleher

tests/data/vcf/1kg_2020_chrM.vcf.gz

@@ -6,7 +6,7 @@
 
 
 @pytest.mark.parametrize(
-    "vcf_file", ["sample.vcf.gz", "1kg_2020_chr20_annotations.bcf"]
+    "vcf_file", ["sample.vcf.gz", "1kg_2020_chr20_annotations.bcf", "1kg_2020_chrM.vcf.gz"]
 )
 @pytest.mark.parametrize("implementation", ["c", "numba"])
 def test_vcf_to_zarr_to_vcf__real_files(shared_datadir, tmp_path, vcf_file, implementation):

tests/data/vcf/1kg_2020_chrM.vcf.gz.csi

@@ -186,7 +186,8 @@ def write_vcf(
 
 def c_chunk_to_vcf(root, v_chunk, contigs, filters, output):
     chrom = contigs[root.variant_contig.blocks[v_chunk]]
-    pos = root.variant_position.blocks[v_chunk]
+    # TODO check we don't truncate silently by doing this
+    pos = root.variant_position.blocks[v_chunk].astype(np.int32)
     id = root.variant_id.blocks[v_chunk].astype("S")
     alleles = root.variant_allele.blocks[v_chunk]
     ref = alleles[:, 0].astype("S")